Everything I've read about them:
1. They were copied from the worst U-boat design of world war 1 - a 1915 model that was designed to be cheap and quick to build because of wartime shortages. It was so bad the German Navy never deployed them, used only for training in the Baltic.
2. All the seals - diving planes, periscope, prop shafts etc. - leaked so badly you couldn't dive below 150 feet. The hull was okay with the pressure, but the pumps could barely keep up with the leaks at 150. Below that the pumps couldn't keep up with the flooding, so if you went to 200 feet you were committed to going all the way down.
Some interesting reading written by the wife of an S boat sailor;
http://www.amazon.com/Pigboat-39-Ame.../dp/081310985X